X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details mixing 6ul [5.8mg/ml Wind in 5mM HEPES pH7.5, 25mM NaCl, 0.0025%(V/V) beta-mercaptoethanol] with 3ul [0.1M MES pH6.1, 0.1M CsCl, 2mM CaCl2, 16%(V/V) PEG 300] cryo-condition: 0.1M Mes pH6.1, 20%(V/V) PEG 300, 10%(V/V)glycerol, 0.1M CsCl, 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.68 α = 90
b = 50.36 β = 112.84
c = 98.62 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH bent mirror 2002-07-31
Diffraction Radiation
Monochromator Protocol
Triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.811 EMBL/DESY, HAMBURG X11

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.9 37.64 99.8 -- 0.0565 -- 4.5 38218 38218 -- -3.0 49.18
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.9 2.0 99.6 -- 0.2759 4.77 3.79 5373

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SIRAS 1.9 35.17 -- 0.0 38216 38216 1859 99.8 0.2179 0.2179 0.21584 0.25571 5%,THIN SHELLS
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9 1.949 2774 97 2677 0.246 0.338 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model individual isotropic B values
Mean Isotropic B 37.247
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.42
Anisotropic B[2][2] -0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 8.304
r_bond_refined_d 0.023
r_angle_refined_deg 2.132
r_dihedral_angle_1_deg 6.619
r_chiral_restr 0.156
r_gen_planes_refined 0.01
r_nbd_refined 0.237
r_xyhbond_nbd_refined 0.159
r_symmetry_vdw_refined 0.202
r_symmetry_hbond_refined 0.23
r_mcbond_it 2.921
r_mcangle_it 4.579
r_scbond_it 5.91
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.163
Luzzati ESD (R-Free Set) 0.152
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3295
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 152

Software

Computing
Computing Package Purpose
MAR Data Reduction (intensity integration)
SCALEPACK, XPREP, CCP4 Data Reduction (data scaling)
SHELXD, SHELXE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement